VIZBI Blog

ECCB paper deadline extended

Seán — Mon, 02 Apr 2012 09:22:55 +0000

Last chance to publish your paper on biodata visualisation at ECCB 2012: in case you missed the March 30 deadline for paper submission, the organisers announced they have extended the deadline to Sunday April 8, 2012 (midnight GMT). For details, see http://www.eccb12.org/proceedings.

ECCB 2012 call for Biodata Visualization papers

Seán — Wed, 14 Mar 2012 17:31:37 +0000

Another key bioinformatics meeting has created a paper track specifically for biodata vis & imaging papers. The European Conference on Computational Biology is the key European computational biology event in 2012, taking place 9-12 September 2012 in Basel, Switzerland. This year, ECCB specifically invites papers on biodata visualisation – the deadline for papers is 30 March 2012.

uPy wins NVIDIA best poster award at VIZBI 2012

Seán — Wed, 14 Mar 2012 09:53:53 +0000

At VIZBI 2012 last week, the NVIDIA award for best poster was decided by popular vote; the winning poster was D18 – uPy: a ubiquitous Python API with biological modeling applications enables ePMV & autoFill by Ludovic Autin, Graham Johnson, Johan Hake, Arthur Olson, Michel Sanner from Scripps & USCF, California, USA. uPy provides a Python interface that lets users drive several computer graphics programs (Blender, Maya, Cinema4D, DejaVu) as well as two Graphical User Interface toolkits (Tkinter and Qt). The uPy group received an NVIDIA Quadro 6000 professional video card, one of the world’s fastest GPUs. Congratulations!

Faster ‘beta’ VIZBI server available

Seán — Mon, 05 Mar 2012 06:00:45 +0000

As the current VIZBI web server has become slow and has had recent crashes, we have been preparing to transfer the site to a new, much faster server. The new server still has minor glitches but is close to fully functional: the speed-up is particularly useful to navigating the VIZBI posters. Thus, we have decided to make it available as a back-up server during VIZBI 2012 under a temporary URL (http://bioviz.info/). Many thanks Jean-Karim Hériché and Venkata Satagopam!

VIZBI 2012 posters now online & zoomable

Seán — Mon, 05 Mar 2012 05:57:41 +0000

VIZBI 2012 posters are now online at http://vizbi.org/Posters/2012; the collection of 75 images and abstracts can be navigated graphically (via image thumbnails), browsed by author or title (via list view), or searched by full text (via VIZBI site search). To help explore these high-resolution images, we made them easily zoomable in any browser using Seadragon Ajax (uses Javascript only, no plugins needed). I believe that in the near future zoomable, high-resolution images will become indispensible in science and beyond; the VIZBI zoomable poster collection can be a showcase, highlighting how this technology can benefit scientific meetings and scientific communication. Many thanks to everyone who contributed, especially Jim Procter & Sven Haag.

NVIDIA Best Poster Award for VIZBI 2012

Seán — Mon, 20 Feb 2012 05:19:56 +0000

We have just confirmed NVIDIA as our latest bronze sponsor, joining Amira and Bitplane, together with our silver sponsor Autodesk. NVIDIA have generously donated a very attractive prize that will be awarded to the best poster at VIZBI 2012: their Quadro 6000 professional video card. One of the world’s fastest GPUs, this card can render 1.3 billion triangles per second, and retails for US$4,999. If you are looking for some extra motivation to improve your VIZBI poster before the submission deadline this weekend, check out these videos demonstrating how the Quadro 6000 can produce photorealistic, interactive 3D scenes as well as detailed, interactive biomedical animations.

2011 Visualization Challenge winners

Seán — Tue, 07 Feb 2012 02:24:26 +0000

Winners of the annual International Science and Engineering Visualization Challenge have just been announced. Outstanding entries featuring biological visualisation include: a video from Graham Johnson (VIZBI 2012 speaker), Andrew Noske, and Bradley Marsh showing a system for interactively visualising cellular compartments (1st Place and People’s Choice); a photograph from Bryan Jones showing a mouse eye with colouring used to highlight 70 distinct cell types (1st Place); a 3D illustration from Andrew Noske, Thomas Deerinck, Horng Ou, and Clodagh O’Shea showing mitosis (People’s Choice); and a poster from Ivan Konstantinov, Yury Stefanov, Alexander Kovalevsky, and Anastasya Bakulina showing the Ebola virus (honourable mention).

Manuel Lima’s ‘Visual Complexity’ book

Seán — Sun, 29 Jan 2012 06:29:57 +0000

In case you missed it, late last year the book Visual Complexity appeared from Manuel Lima (VIZBI 2011 keynote speaker), and has been very well received.

Drew Berry’s ‘Hollow’ video

Seán — Sun, 29 Jan 2012 06:13:56 +0000

A few months ago, Drew Berry released a video with the musician Björk for her song ‘Hollow’ from the album ‘Biophilia’. The video features a beautiful collection of cellular and molecular animations, smoothly zooming between scales, plus a homage to the fruit portraits of Giuseppe Arcimboldo. I highly recommend tracking down the ‘Hollow’ video – it’s great for engaging friends and colleagues; you can probably find it on YouTube, but it is best viewed on an iPad or iPhone, where it has been released as part of the Biophilia app. You can access a preview of the video here.

E.O. Wilson’s Life on Earth

Seán — Sun, 29 Jan 2012 05:59:35 +0000

Last week, Apple announced several upcoming iPad textbooks that promise a new level of engagement and interactivity: one of the books - E.O. Wilson’s Life on Earth – is being lead by Gaël McGill (VIZBI 2011 speaker and VIZBI 2012 tutor) together with Drew Berry (VIZBI 2011 keynote speaker) as animation director.

Some CPP fellowships still available

Seán — Sun, 29 Jan 2012 05:48:03 +0000

For participants facing financial difficulties, a limited number of fellowships are still available that effectively provide free registration. The remaining fellowships will be awarded on a first-come, first-served basis. To apply, you must submit a poster and application letter – see the CPP section of the VIZBI registration page for details.

Last day for VIZBI 2012 early registration

Seán — Sun, 29 Jan 2012 05:45:01 +0000

As VIZBI 2012 draws nearer, a quick reminder that early registration closes at midnight today (January 29) in any time zone. After this date, registration costs €50 more.

VIZBI 2012 early registration closes soon!

Seán — Thu, 12 Jan 2012 10:37:13 +0000

A quick reminder that early registration for VIZBI 2012 closes in just under three weeks: the deadline is midnight on January 29 in any time zone. After this date, registration costs €50 more. The deadline for poster submission is 26 February 2012.

Last day for free registration at VIZBI 2012

Seán — Fri, 06 Jan 2012 01:13:05 +0000

For VIZBI 2012, a limited number of free registrations are offered to students via the EMBL’s Corporate Partnership Programme. To be eligible, students need to submit a poster for VIZBI 2012 before January 7 at 12 noon UTC/GMT. For details, see here.

Last call for ISMB 2012 papers on biovis

Seán — Fri, 06 Jan 2012 00:59:15 +0000

A quick reminder that next Friday, January 13 is the deadline for submitting your work on Biological Data Visualization or Bioimaging to the upcoming Intelligent Systems for Molecular Biology (ISMB) in Long Beach, California (USA) July 15-17, 2012. Presenters of accepted papers are given a 20-minute speaking slot (plus 5 minutes for questions) in the conference schedule. Accepted papers will be published in an online part of the journal Bioinformatics, resulting in fully citable articles indexed by Medline and ISI. More information about ISMB paper submission is at:

http://www.iscb.org/ismb2012-submission/ismb2012-call-for-proceedings

Biovis positions available in Sydney

Seán — Sat, 22 Oct 2011 22:08:42 +0000

Looking for a new career opportunity in biovis, either for yourself or a colleague? I am starting a new lab in Sydney focused on biological data visualization and I have a range of postdoc and programmer positions to offer – either at junior or senior level – as well as PhD studentships. The lab will be jointly associated with the Garvan medical research institute and with the CSIRO division of Mathematics, Informatics, and Statistics. A primary focus of the lab will be on using principles of usability, data visualization, and graphic design to develop state-of-the-art methods and tools that address cutting edge challenges in basic biomedical research. A second focus of the lab will be on using these methods to analyse experimental datasets in collaboration with groups at the Garvan. Projects will include leading the VIZBI initiative, leading user-interface development for the Reflect project (currently used to analyse ~20,000 documents per day), and developing methods for integrating 3D structures with genomics, proteomics, and other systems biology data: for further details see odonoghuelab.org.

I am seeking to recruit people with a range of skill sets, including a Javascript architect, a Java3D programmer interested in molecular graphics, plus several bioinformaticians and data visualization experts. The postdoc and programmer positions will be initially for five years, but may potentially be extended. Academic salaries in Australia are among the best in the world, and both CSIRO and Garvan both offer salaries, relocation and other benefits that are above the Australian average.

So, if you know anyone matching the above profiles who may be interested to work in one of the world’s most beautiful, lively, and livable cities, please put them in touch (sean@odonoghuelab.org). I will be attending BioVis/VisWeek and will be available from Oct 22-25 to meet and provide further details about these positions.

ISMB 2012 call for Biodata Visualization papers

Seán — Thu, 13 Oct 2011 16:52:31 +0000

You are invited to consider submitting your work on Biological Data Visualization or Bioimaging to the upcoming Intelligent Systems for Molecular Biology (ISMB) meeting, to be held in Long Beach, California (USA) July 15-17, 2012. ISMB is organized by the International Society for Computational Biology, and is the most prominent and selective computational biology conference each year. Previous ISMB meetings have attracted over 230 submissions and had an acceptance rate between 15-20%. Accepted papers are invited to give talks at the main meeting, and are published in a special issue of the journal Bioinformatics.

Traditionally ISMB has had very few papers on biodata visualization or bioimage informatics, with only a scattered talk here and there or an occasional special session or workshop. One key reason for this was that there was no heading under which such papers could be submitted and reviewed properly. Therefore, in 2010, a “Bioimaging” track was added (chaired by Gene Myers and Bob Murphy) to encourage submission of papers and provide appropriate reviewing. It received an excellent response from the community, both in terms of people willing to serve on the program committee and papers submitted.

For ISMB 2012, the scope of the track has been broadened to “Bioimaging and Data Visualization”, and is being chaired by Robert Murphy and myself: we would now like to get the word out about the track so that people are aware of it and of the submission deadline.

Submission for ISMB papers opens soon, and the deadline for submission will be January 13, 2012 (with notification of decisions on March 16th). Please note that selection from submitted papers is the primary mechanism for choosing talks at the meeting, and that initial submissions do not have to be in the final OUP format. The focus during the initial review is on the quality of the work, with easily fixable problems with presentation not given too much weight. Presenters of accepted papers will be given a 20-minute time slot (plus 5 minutes for questions) in the conference schedule. Accepted papers will be published in an online part of the journal Bioinformatics, resulting in fully citable articles indexed by Medline and ISI. More information about ISMB paper submission is at:

http://www.iscb.org/ismb2012-submission/ismb2012-call-for-proceedings

We hope that you will consider submitting some of your best work to the track. Having a large number of submissions and accepted papers will be critical to continuing it at ISMB. We believe that it is very important for the broader computational biology community to be aware of the exciting results being generated in the areas of bioimaging and biodata visualization, and of the important role these results play in advancing our understanding of biology.

Nature Methods article on layout principles

Seán — Thu, 29 Sep 2011 18:43:09 +0000

In the current issue of Nature Methods, Bang Wong has a useful 1-page article summarizing key principles for laying out text and graphics.

NSF & AAAS Science Visualization Challenge 2011

Seán — Mon, 12 Sep 2011 10:00:57 +0000

The National Science Foundation (NSF) and the journal Science have announced the 2011 International Science & Engineering Visualization Challenge. Entries due 30 September 2011.

New VIZBI website

Seán — Fri, 09 Sep 2011 12:00:13 +0000

We have completely updated the VIZBI website with a new design and some new features, including a video gallery, an improved poster gallery (including now thumbnails from the 2010 posters), galleries of photographs from 2011 and 2010, as well as information about the upcoming VIZBI 2012 conference. Check it out! Thanks especially to Christian Stolte for the great design, also to Janos Binder for help with Javascript.

VIZBI 2012 call for participation

Seán — Thu, 08 Sep 2011 17:17:43 +0000

We are delighted to announce VIZBI 2012 (http://vizbi.org/2012/), the 3rd international meeting on ‘Visualizing Biological Data’ – and the first in a series of EMBO conferences on this topic – to be held at the European Molecular Biology Laboratory, Heidelberg (Germany), 6-8 March, 2012. VIZBI 2012 brings together scientists actively using or developing computational visualization to study a diverse range of biological data; the conference also attracts participation from medical illustrators, graphic designers, and graphic artists. VIZBI 2012 features 22 invited talks from high-profile speakers that will review the state-of-the-art and challenges in visualizing data from genomes, transcripts, proteins, cells, organisms, and populations. Prior to the meeting (5 March), there will also be tutorials on visualization tools & methods. All VIZBI participants have the opportunity to present a poster describing their work. Just before your poster session, you will be given ~60 seconds and 2 PowerPoint slides to briefly introduce yourself and your poster to all VIZBI participants (details here). If you cannot join us in Heidelberg, you have the option of virtual registration, which allows participation via streaming video and chat. Registration is now open, and early registration closes 29 January 2012. The first two VIZBI meetings were timely and energized and have fostered some significant advances in the field; VIZBI 2012 promises no less, and is supported by a greatly expanded organizing team – we hope you can join us for this exciting event!

Slides from the VIZBI 2011 talks

Seán — Thu, 25 Aug 2011 00:51:31 +0000

Now available for download in PDF or PPT format are slides for the following VIZBI 2011 talks: Yoseph Barash, Susumu Goto, Des Higgins, Robert Macleod, Tamara Munzner, Rod Page, John Quakenbush, Herve Tettelin, and Eric Westhof. These slides can also be downloaded from the corresponding video pages.

In addition, slides are also available from the recent workshop on “Data visualization and user interfaces” at ISMB 2011. There were talks on user interfaces by Scooter Morris, on data visualization by Nils Gehlenborg, on visual analytics by Carsten Goerg, and some discussion points by myself.

Seeking Processing.js tutor for VIZBI 2012

Seán — Mon, 22 Aug 2011 14:15:40 +0000

We are seeking someone to give a hands-on, 1/2-day tutorial on Processing.js as part of the VIZBI 2012 tutorial day (Monday, 5 March 2012, in Heidelberg, Germany). At VIZBI 2011, we offered tutorials for the first time and they were quite popular, with the Processing tutorial attracting the most students. For VIZBI 2012 we would like to offer a Processing.js tutorial; the tutor will receive a share of the tutorial registration fee plus a complementary pass to the VIZBI conference, which takes place on the three days following the tutorial day. To get a flavor of the conference, check out the videos from previous VIZBI meetings. If you are interested in this opportunity, or if you can suggest someone ideal for spreading the word about Processing.js to computational biologists, please get in touch:

ISMB 2011 workshop on data vis & UIs

Seán — Mon, 18 Jul 2011 05:13:19 +0000

If you are attending ISMB 2011 in Vienna, don’t miss today’s 2-hour workshop on “Data visualization and user interfaces”:

Date: Monday, July 18
Time: 10:45 a.m. – 12:40 p.m.
Room: Hall N/O

10:45 – 11:10 User Interface Design (Speaker: Scooter Morris)
11:15 – 11:40 Data Visualization (Speaker: Nils Gehlenborg)
11:45 – 12:10 Visual Analytics (Speaker: Carsten Görg)
12:15 – 12:40 Discussion (Moderator: Seán O’Donoghue)

VIZBI 2012 and beyond

Seán — Wed, 13 Jul 2011 19:34:13 +0000

Eric Lander’s opening remarks elegantly articulated the urgent need for an increased focus on data visualization in biological research, and, from the strong positive feedback, it’s clear that VIZBI helps address this need. The first VIZBI meeting was an experiment – it was not certain if this very diverse group would want, need, or be able to effectively communicate, let alone collaborate. However it is now clear the experiment is a success: the two meetings so far have already led to many fruitful collaborations and outcomes. Personally, I was also surprised to see that a large number of participants from 2010 came again in 2011, including many from Europe and even more remote places like Australia: clearly VIZBI has already begun to form a community, and indeed many people suggested that the website evolves to support this. Thus, the need to continue VIZBI is clear: now, what about the means to do so?

Here, I am delighted to report good news: EMBO recently accepted our application to start a VIZBI conference series at EMBL, Heidelberg. Together with the NIH grant awarded last year for a VIZBI conference series at the Broad Institute, we now have funds to run VIZBI annually – alternating between Europe and the USA – until at least 2016. We are now enlarging the organizing team and improving aspects of the meeting, especially the website. We are also finalizing the program for VIZBI 2012, which will be held 6-8 March 2012 at the EMBL in Heidelberg, Germany. As with previous years, VIZBI 2012 will have outstanding speakers, and will give all participants the opportunity to present their work via the fast-forward and poster sessions. For some, traveling to Heidelberg is difficult, so we plan to offer virtual participation via streaming video and chat. We will announce the detailed VIZBI 2012 program in August. Until then, together with the 2012 organizing team, I look forward to meeting many of you again in Heidelberg, 6-8 March 2012.

Videos of VIZBI 2011 talks now available

Seán — Tue, 12 Jul 2011 23:48:46 +0000

Videos of the VIZBI 2011 talks are now available at http://vizbi.org/videos/. These are high-quality video recordings of great presentations from outstanding scientists: feel free to share the videos with colleagues. I would like to thank again all who made this possible, especially the speakers, Lars-Erik Siren from the Broad for his dedicated video-production work, and the VIZBI 2011 co-chairs Jim Procter, Lawrence Hunter, and particularly Bang Wong for engaging the full support of the Broad Institute.

Illumina iDEA Conference

Seán — Fri, 08 Apr 2011 21:00:36 +0000

Illumina have announced the iDEA Conference (June 14–15, 2011, San Diego), where finalists in the iDEA Challenge will present their approaches to analyzing, visualizing, and interpreting next-generation sequencing data. The iDEA Conference is open to anyone interested in methods for understanding data produced by next-generation sequencing and high-density array studies. The iDEA Challenge winners will be announced at the conference.

VIZBI 2011 Feedback

Seán — Thu, 07 Apr 2011 21:00:40 +0000

The image below summarizes the feedback received from VIZBI participants. Many thanks to everyone that submitted feedback, especially those who took time to give specific suggestions for improvement. Overall, the feedback is clearly very positive and quite consistent across both VIZBI meetings so far, indicating that the VIZBI format addresses an important and largely unmet need. On behalf of the VIZBI organizers, I would like to thank again the speakers, session chairs, poster presenters, tutors, and all who contributed to making VIZBI 2011 a very exciting and engaging meeting. We hope you can join us for VIZBI 2012 (March 6-8) at the EMBL in Heidelberg, Germany, or again in 2013, when VIZBI returns to the Broad in Cambridge, MA, USA.

1st IEEE Symposium on Biological Data Vis.

Seán — Wed, 06 Apr 2011 22:00:44 +0000

We are delighted to announce the call for participation for the 1st IEEE Symposium on Biological Data Visualization (BioVis 2011), 23-24 October 2011 in Providence, RI, USA, which will be co-located with IEEE VisWeek 2011. BioVis is designed to appeal to all interested in biological data visualization, and especially for researchers in computer science, bioinformatics, and biology who are involved in the design, implementation, application, and evaluation of novel visualization techniques and interested in the theoretical foundations underlying these topics. It features a full paper track, in which the best submissions are presented as talks and published as part of the meeting proceedings. BioVis is planned to complement the VIZBI meetings, which lack a paper track, and are instead organized in a format more typical for biology conferences. Whereas VIZBI aims to review current visualization methods, tools, and challenges in biology, BioVis aims to present novel approaches to these challenges. The VIZBI and BioVis organizers plan to actively encourage an ongoing dialog and exchange between the two meetings, e.g., by sharing invited speakers. The deadline for paper submission is 30 April 2011, and for abstracts is 8 July 2011.

VIZBI 2011 posters

Seán — Tue, 05 Apr 2011 21:16:16 +0000

The VIZBI 2011 posters can now be browsed visually via thumbnails at: http://vizbi.org/2011/Posters.

VIZBI 2011 photos on flickr

Seán — Fri, 01 Apr 2011 11:21:52 +0000

There are already around 40 photos from VIZBI 2011 on flickr. If you have additional photos of VIZBI 2011, we encourage you to put them up on flickr and tag them with both ‘VIZBI’ and ‘VIZBI2011′. Some examples:

Bioinform article about VIZBI 2011

Seán — Thu, 31 Mar 2011 14:53:23 +0000

Last week, the online publication Bioinform from GenomeWeb released a 850-word article about VIZBI 2011. A subscription is required to access the full article.

VIZBI 2011 poster prize winner!

Seán — Sat, 26 Mar 2011 13:23:26 +0000

The winner of the VIZBI 2011 poster prize goes to Jörg Bernhardt (E.M.A.-University Greifswald, Germany) for his poster titled ‘OntologyMaps’, co-authored with Henry Mehlan, Julia Schüler, and Michael Hecker – congratulations Jörg!

Abstract submissions now open for iEvoBio 2011

Jim — Thu, 17 Feb 2011 10:15:18 +0000

Rod Page, who will speak during the Population data session at this year’s VIZBI, is also involved with iEvoBio, a conference on Informatics for Phylogenetics, Evolution, and Biodiversity, which – like VIZBI, is now in its second year.

iEvoBio 2011 will take place in Norman, Oklahoma, in the US, from the 21st to the 22nd June, and is now accepting submissions for informatics talks concerning new tools, cyberinfrastructure development, large-scale data analysis, and visualization. iEvoBio and its sponsors strongly support open-source software development, and where appropriate, submissions must provide full details of their software’s licensing terms.

The submission deadline for full papers is 18th March 2011. For further details, please go to http://ievobio.org/ocs/index.php/ievobio/2011.

VIZBI early registration closes Jan 31

Seán — Tue, 25 Jan 2011 12:22:29 +0000

A quick heads-up: the early registration for VIZBI 2011 closes next Monday (Jan 31) – after this date, registration costs $100 more.

Biological visualization in the New York Times

Seán — Mon, 22 Nov 2010 03:00:15 +0000

The New York Times website recently posted a video titled ‘The Animators of Life‘, about recent work by scientists and animators in creating vivid depictions of molecular processes occurring inside living cells. The New York Times video features work by Drew Berry, and relates to work by Gaël McGill, both speakers at VIZBI 2011.

VIZBI 2011 registration now open

Seán — Tue, 16 Nov 2010 18:53:29 +0000

Registration is now open for VIZBI 2011 at http://vizbi.org/2011/Registration/. Due to the venue size, we are strictly limited to a maximum of 250 participants. Book early to ensure your place, and to take advantage of the early registration fee.

VIZBI 2011 call for participation

Seán — Fri, 05 Nov 2010 00:07:18 +0000

We are delighted to announce VIZBI 2011, the 2nd workshop on ‘Visualizing Biological Data’, to be held at the Broad Institute, Cambridge-MA (USA), March 16-18, 2011. VIZBI 2011 brings together scientists actively using or developing computational visualization to study a diverse range of biological data. The workshop features an impressive list of high-profile speakers who will each review the state-of-the-art and challenges with visualization in their field. VIZBI 2011 also features an art and science evening (Thursday) during which we will be joined by medical illustrators, graphic designers, and artists interested in biological visualization. On Saturday, March 20, immediately after the workshop, participants can choose from a range of tutorials and take part in a hands-on ‘bring-your-own-data’ session. All workshop participants are encouraged to submit a poster on their work, plus an image for the art & science evening. Participants also have the opportunity to be part of an authoritative book co-authored with the VIZBI speakers; the book will be the first to comprehensively review this topic – essentially an expanded version of the Nature Methods focus issue – and will be distributed by a major scientific publisher. We hope you can join us for this exciting event!

The VIZBI 2011 chairs
Seán O’Donoghue, EMBL
James Procter, U. Dundee
Larry Hunter, U. Colorado
Bang Wong, Broad

Illumina’s iDEA Challenge

Seán — Sun, 31 Oct 2010 22:53:16 +0000

The company Illumina recently announced their ‘iDEA challenge’ to recognize new, creative ideas on how to visualize and analyze genomics data. Entries are due March 15, 2011 and the winners will be announced June 15, 2011. The winning academic entry will be awarded US$50,000, while the winning commercial entry will be awarded a co-marketing agreement with Illumina. Seperate prizes will also be awarded for the most creative visualization, and most creative algorithm. If you are working on visualizing genome data, it sounds like a great opportunity to achieve recognition.

VIZBI 2011 speaker wins MacArthur Fellow

Seán — Wed, 13 Oct 2010 11:55:48 +0000

Drew Berry, a VIZBI 2011 keynote speaker, has been awarded a MacArthur Fellow. He is a animator who uses scientifically accurate and aesthetically rich visualizations to elucidate cellular and molecular processes for a wide range of audiences. A video about the award is available here that includes an interview with Dr Berry, and features some of his work.

Visualizing Macromolecular Complexes and Cellular Structures

Seán — Sat, 07 Aug 2010 16:52:34 +0000

A Workshop on Recent Advances and Future Prospects for Visualizing Macromolecular Complexes and Cellular Structures is planned for Oct 12-13 at the NIH in Bethesda, Maryland, USA. Invitations to submit abstracts are now open – for more details, see https://respond.niaid.nih.gov/conferences/

Article about VIZBI 2010

Seán — Thu, 05 Aug 2010 15:23:43 +0000

David Leader - one of the participants in VIZBI 2010 – wrote a short article about the workshop in The Biochemist http://www.biochemist.org/bio/03204/0041/032040041.pdf

Use of Colors in Figures

Seán — Wed, 04 Aug 2010 16:38:04 +0000

Bang Wong just published an interesting article in Nature Methods on the use of colors in figures – http://www.nature.com/nmeth/journal/v7/n8/full/nmeth0810-573.html
Actually this is planned to be the first in a series of regular ‘graphical tips’ in Nature Methods, a plan that was hatched at VIZBI 2010.

BBSRC/AHRC Workshop on “The challenges of Visualising Biological Data”

Nils — Wed, 14 Jul 2010 12:21:15 +0000

The BBSRC and the Arts & Humanities Research Council (AHRC) wish to invite applications to attend a multi-disciplinary workshop exploring the challenges of visualising increasingly complex and large-scale biological datasets.

The workshop will take place in Bristol (UK) on November 16th and 17th 2010. Applications are due on August 6th at 4 PM.

Full details are on the workshop website.

ISMB ‘Birds of a Feather’ on Visualization

Seán — Mon, 12 Jul 2010 16:24:10 +0000

At the ISMB 2010 ‘Birds of a Feather’ (BoF) later today, we will lead a discussion through a range of topics related to the major challenges in visualization, plus current and future the community efforts towards meeting these challenges. Notes from the meeting will be available at a Google doc here – any BoF participant that want to contribute to writing this document is welcome – just write to to be added as an author of the document.

11 more VIZBI videos now available

Seán — Mon, 12 Jul 2010 14:31:10 +0000

Chris North

Ben Fry

Ivica Letunic

Eric Westhof

Inna Dubchak

Ting Wang

Michael Nilges

Oliver Kohlbacher

Nitin Baliga

Anne Carpenter

Mark Bastin

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Join the VIZBI ‘Birds of a Feather’ at ISMB

Seán — Thu, 08 Jul 2010 03:59:43 +0000

At ISMB 2010 we will be hosting a 1-hour ‘Birds of a Feather’ discussion on visualizing biological data (see here for details). We plan to cover the major visualization challenges identified in VIZBI 2010, and to discuss community efforts aimed at improving integration, effectiveness, and usability of visualization in biology. Please contact us if you would like to propose topics or disseminate announcements. All are welcome!

Time: Monday, July 12, 6:00 p.m. – 7:00 p.m.
Room: 304

UK Meeting call for participation: Challenges of visualising biological data

Seán — Wed, 30 Jun 2010 16:28:13 +0000

The UK’s Biotechnology and Biological Sciences Research Council is organising a meeting to explore the challenges of visualising biological data. The registration deadline is the 6th August 2010.

Call for submissions to iEvoBio: New methods for visualizing evolution

Seán — Tue, 27 Apr 2010 08:59:56 +0000

iEvoBio is short for ‘Informatics for Phylogenetics, Evolution and Biodiversity’, and is a new meeting which is being held as a satellite of the Evolution 2010 meeting which takes place in Portland, Oregon (US) this year.

iEvoBio takes place from June 29-30th and provides a forum for mathematicians, software developers, bionformaticians and evolutionary and computational biologists to discuss their work. The meeting includes a software bazaar and a challenge session, which is focused this year on exploring new methods for the visualization of evolution.

The deadline for submissions to the iEvoBio Visualization Challenge and the Software Bazaar is 21st June 2010.

Two videos and more photos from VIZBI 2010

Seán — Thu, 22 Apr 2010 00:56:54 +0000

Reactions to the Nature Method special issue

Seán — Fri, 16 Apr 2010 15:52:52 +0000

In preparing the Nature Methods special issue on visualizing biological data, our goal was to create a useful resource for the experimental biology community. In the last month since it was published, there are indications that it is having an impact. It was featured prominently on the websites of Nature and Nature Biotechnology, and has also been featured on several blogs related to visualization and biology: e.g., Vizworld, Bioephemera, Timothy M. Kunau, ISPRS WG II/6 blog on Geographical Visualization and Virtual Reality, Getting Genetics Done, HENRY, Vallve’s Blog, QuimBiología, and Serialized Thoughts. In addition the special issue was covered in several FriendFeeds from Simon Cockell, Brad Chapman, and Abhishek Tiwari (who runs an interesting blog called fisheye perspective on visual analytics and bioinformatics). The issue was also covered by tweetmeme from joergkurtwegner. The PDFs from the special issue are still freely available, but I believe that soon they will be available only to Nature Methods subscribers – so best to grab them now if you want them, and tell any colleagues who may be interested.

Meetings about visualizing biological data

Seán — Tue, 13 Apr 2010 16:31:33 +0000

Here are links to upcoming or recent meetings that include talks or sessions related to both visualization and biology. If you know of others, leave a comment or contact me and I’ll add them to this post. Eventually this post will probably evolve into a separate page.

ISMB Special Session on Network Visualization

Nils — Wed, 07 Apr 2010 22:29:08 +0000

ISMB 2010 in Boston will feature a special session on visualization of biological networks. The session will focus on the discussion of use cases and standardization of input and output, as well as integration of tools. More background and details about the session are available on the ISMB 2010 website.

VCBM 2010 Poster Deadline Extended

Nils — Wed, 31 Mar 2010 21:05:07 +0000

The poster submission deadline for the 2nd Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) has been moved to May 5, 2010.

The workshop will be held in Leipzig, Germany, on July 1-2, 2010 and will address the integration of state-of-the-art visualization and image analysis for application to research in biology and medicine.

Wikipedia and biological data visualization

Seán — Mon, 29 Mar 2010 20:23:36 +0000

You may be interested in some Wikipedia pages we started that aim to provide a comprehensive list of computational tools for visualizing biological data. Starting from http://en.wikipedia.org/wiki/Biological_data_visualization you can access lists of tools for different areas, e.g., alignment, phylogeny, molecular graphics. The pages for systems biology and microscopy currently have only very few tools, and for MRI there is currently no ‘list of’ page. So, we encourage everyone to add their favorite tools! This will give visibility to your favorite tools, and will make these Wikipedia pages a more valuable resource for the community.

Actually there is a back-story to these pages: due to space limitations, in the Nature Method special issue we were very restricted in the number of visualization tools we could mention. As a result, the list of tools cited was ultimately a subjective selection. This was a bit frustrating, as we were forced to remove for the tables several tools we liked. Thus the idea came about to create a more comprehensive list of visualization tools in each field. And the Wikipedia ‘list of’ pages seemed like an ideal place.

Video of VIZBI closing remarks

Seán — Mon, 29 Mar 2010 00:59:27 +0000

In this video of the final 30 minutes of VIZBI, the session chairs shared their impressions of the most important themes and challenges to emerge during the meeting.

VIZBI 2010 photos on flickr

Seán — Sat, 27 Mar 2010 17:21:24 +0000

There are already some photos from VIZBI 2010 on flickr – we would encourage others to put their photos there and use both tags ‘vizbi2010′ and ‘vizbi’ – here are some examples:

Please update your RSS feed source

Seán — Thu, 25 Mar 2010 17:27:39 +0000

We have now switched to using http://feeds.feedburner.com/vizbi – please update your RSS reader to be sure you get all future blog entries.

Science & Engineering Visualization Challenge

Seán — Wed, 24 Mar 2010 20:20:12 +0000

In case you missed it, here are the winners of the 2009 international Science & Engineering Visualization Challenge.

VIZBI blog on Twitter, Friendfeed & Facebook

Nils — Wed, 24 Mar 2010 15:12:48 +0000

If you want to stay up to date on everything VIZBI-related and get news about similar events, start following our Twitter feed: http://www.twitter.com/vizbi or our Friendfeed: http://friendfeed.com/vizbi, or on Facebook. This is in addition to the VIZBI wiki http://www.na-mic.org/Wiki/index.php/VIZBI2010.

Art, Science & Visual Communication

Seán — Mon, 22 Mar 2010 21:14:51 +0000

This week in Cambridge, UK, is a 2-day meeting on science, art and visualisation called ‘Have you seen a molecule’

Please give feedback to EMBO before 15 March

Seán — Fri, 05 Mar 2010 12:07:16 +0000

The VIZBI workshop was funded by the EMBO and they would now like your feedback before 15 March 2010. Please take the time to fill out the EMBO questionnaire. It is very important that EMBO receives feedback from as many participants as possible, as this information will strongly influence their decision to fund any future VIZBI meetings.

In addition, you are also encouraged to send any comments, suggestions, or criticisms about the workshop directly to VIZBI committee. We can be reached at the following email address:

VIZBI prize winner!

Seán — Fri, 05 Mar 2010 11:59:54 +0000

The winner of the first VIZBI prize goes to Christian Grove (California Institute of Technology, Arcadia, United States of America) for his poster on the Virtual Worm, co-authored with Paul Sternberg – congratulations Christian!

VIZBI prize finalists

Seán — Thu, 04 Mar 2010 08:13:40 +0000

Together with the session chairs, the five images+abstract below have been selected as finalists for the VIZBI prize. The final winner will be announced after Bang Wong’s keynote talk later today.

Silverlight anyone?

Seán — Wed, 03 Mar 2010 21:17:37 +0000

We are planning to put the VIZBI poster images in Microsoft Silverlight. If anyone at VIZBI has (or would like to have) experience in Silverlight please contact Jim.

VIZBI Wiki

Seán — Wed, 03 Mar 2010 20:54:55 +0000

Following a conversation with Steve Pieper, he set up a Wiki and has invited VIZBI participants to use it for sharing their notes on VIZBI. I’m planning to post to it – feel free to join: http://www.na-mic.org/Wiki/index.php/VIZBI2010. To edit this wiki, you need to create an account (to fight spam) – just be sure to mention you are associated with the VIZBI meeting when you make an account. Thanks Steve!

Visual Computing for Biology & Medicine

Nils — Wed, 03 Mar 2010 12:41:46 +0000

Paper submissions to the 2nd Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) are still possible until March 8th. Posters can be submitted until April 19th. The workshop will be held in Leipzig, Germany, on July 1-2, 2010. Full details are available on the website: http://www.vcbm.org/2010

VIZBI FriendFeed Group

Nils — Wed, 03 Mar 2010 05:45:22 +0000

We have opened a VIZBI 2010 group on FriendFeed. Please join and add your own comments about the talks at http://friendfeed.com/vizbi2010.

Nature Methods special issue

Seán — Mon, 01 Mar 2010 13:07:41 +0000

Over the last six months we have been working with a group of scientists, including the VIZBI speakers and others, to prepare a series of reviews on visualizing biological data. Today these reviews have been published in a supplementary issue of Nature Methods (Volume 7 No 3 ppS1-S68). In addition to five reviews covering visualization of data from systems biology, genomics, 3D macromolecular structures, alignments and phylogenies, and image-data, the supplement also contains a commentary on future visualization. The editors have also written a 1-page forward and 2-page summary of all reviews. Thanks again to Bang Wong for help with the cover image. We have written the reviews to be understandable to beginners as well as credible to experts. We believe this collection will be a valuable resource for the community of life scientists using visualization as part of their research.

Welcome to the VIZBI blog

Seán — Sun, 28 Feb 2010 10:12:51 +0000

Our primary goal in the VIZBI workshops is to bring together researchers using and developing methods to visualize a broad range of biological data. Our focus is on the visualization of processed and annotated data in their biological context, rather than the processing of raw data, or on experimental visualization techniques.

Having called together this community, we are now providing this blog as a way of staying in contact. We plan to post here announcements related to the VIZBI meeting, e.g., the publication of articles and videos related of the VIZBI talks. We also plan to post information not strictly related to the VIZBI meeting, but of interest to the VIZBI community, e.g., announcements of other similar meetings, news about other significant publications, or the launch of new web resources related to visualizing biological data.

In addition, we hope that the blog can be used for discussions that help to identify and exploit synergies between visualization in different areas of research. For example – cases for inter-operation, the re-use of methods or concepts, and common conventions in usability.

Thus, we would like to invite you to contact us if you have news, announcements, or topics you would like to add to the VIZBI blog.